Solution and solid-state spectra of quinacridone derivatives as viewed from the intermolecular hydrogen bond

Quinacridones are industrially important hydrogen-bonded pigments. The color in the solid state is vivid red, while it is pale yellow in solution, indicating evidently the involvement of intermolecular interactions in the solid state. The electronic structure has therefore been investigated with special attention to the role of intermolecular NH...O hydrogen bonds for three representative quinacridone compounds with different hydrogen-bond forming characteristics: unsubstituted gamma-quinacridone (gamma-QA) with two NH groups, mono-N-methylquinacridone (MMQA) with one NH and one CH(3), and N,N'-dimethyl-quinacridone (DMQA) with two CH(3) groups. The number of the NH...O hydrogen bonds per molecule is four, two, and zero for gamma-QA, MMQA, and DMQA, respectively. In solution, no significant difference in absorption maximum is recognized between gamma-QA, MMQA, and DMQA. However, in the solid state, the absorption maximum of gamma-QA appears at the longest wavelength, followed by MMQA and then DMQA, depending on the number of NH...O intermolecular hydrogen bonds. The role of the hydrogen bond is found to align transition dipoles in a "head-to-tail" fashion and to displace the absorption band toward longer wavelengths due to excitonic interactions. The extent of the spectral shift increases with increasing number of hydrogen bonds per molecule.     

Geometry and electronic structure of the dimethyl sulfoxide dimer. Calculation by the MNDO method

The geometric and electronic structure of the complex formed by dipole-dipole interaction between two molecules of DMSO in the "head-to-tail" orientation were calculated by the MNDO quantum-chemical method. The minimum total energy corresponds to a distance of 5.5 Å between the sulfur atoms, and the angle between the axis of the molecular dipoles is 16.4°. This agrees with calculations for liquid DMSO by molecular dynamics. The large equilibrium distance between the DMSO molecules explains its low density in the liquid phase and the high intensity of microwave absorption due to free volume sufficient for rotation of one molecule in the complex in relation to the dipole axis of the other.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117334 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1340–1344, June, 1992.     

The crystal structure of octakispentoxy-phthalocyaninatocopper with pyridines axially substituted: the molecules stacked with J-aggregates

For coordination with two pyridines at the axis, the ring skeleton of octakispentoxyphthalo- cyaninatocopper maintains planar conformation, different from the structure of octakisbutoxy- phthalocyaninatocopper reported previously. The structure shows all molecules stacked along the b axis to form a one-dimensional molecular chain; neighboring molecules in the chain are arranged as J-aggregates, consistent with its crystal diffuse reflectance spectroscopy (DRS) having a red shift compared with its electronic absorption spectroscopy in pyridine.     

Elusive forms and structures of N-hydroxyphthalimide: the colorless and yellow crystal forms of N-hydroxyphthalimide

A comprehensive structural characterization of the colorless and yellow forms of N-hydroxyphthalimide (NHP), the deuterated form (NDP), and the ethoxylated form (ethoxy-NHP) has been carried out using single-crystal X-ray diffraction, FTIR and Raman spectroscopies, and scanning electron microscopy. Both NHP and NDP forms crystallize in the monoclinic space group (P21/c, No. 14). The various forms of NHP differ in the way in which the molecules adjoin one another through their N-hydroxyl groups and how the carbonyls of the isoindole-1,3-dione ring differ through intermolecular hydrogen bonding. Although the hydrogen bonding about the b axis is virtually the same, the isoindole-1,3-dione ring experiences different twists for the two NHP forms. Both the colorless and yellow forms of NHP exhibit strong intermolecular hydrogen bonding between O(3) and H(1). In the yellow form, the N-hydroxyl group is significantly out of the plane (approximately 1.19 degrees ), but the N-hydroxyl group in the colorless form is only approximately 0.06 degrees out of the plane. Both forms of NHP reveal an infinite chain of intermolecular hydrogen-bonded molecules in the direction of the b axis; however, the molecules are ordered differently within the unit cells. The hydrogen-bond geometry for the yellow form of NHP is O(2)-H(1)...O(3), with an angle of 185 degrees , intermolecular distances of O(2)...O(3) = 2.68 A and H(1)...O(3) = 1.70 A, and an intramolecular hydrogen bond of O(1)...H(1) = 1.17 A. The colorless form of NHP shows an intermolecular hydrogen-bond geometry between O(3) and H(1) with a distance of 1.78 A; the O(2)-O(3) distance is 2.71 A. The O(2)-H(1)...O(3) angle is 159 degrees, and the intramolecular distance is O(1)...H(1) = 0.97 A. The N-ethoxy derivative of NHP crystallizes in an orthorhombic space group (Pnma, No. 62) and exhibits no hydrogen bonding, displaying a strong head-to-tail stacking of the planar rings along the needle axis direction.     

High guest inclusion in 3β-amino-7α,12α-dihydroxycholan-24-oic acid enabled by charge-assisted hydrogen bonds

3β-Amino-7α,12α-dihydroxycholan-24-oic acid (2) forms inclusion compounds with high ratio (host/guest=1/4) of guest methanol. Both hydrogen bonds and hydrophobic interactions are important to the solid structure. The cholates assemble in a head-to-tail fashion to form infinite hydrogen-bonded chains. The chains are interconnected between cholates and also through the guests. Large channels are formed along the crystallographic a axis where most of the methanol molecules are located. Presence of a dominant hydrogen-bonding motif (i.e., ammonium-carboxylate ion pairing) is probably responsible for high guest incorporation.     

Highly Efficient Non‐Palladium‐Catalyzed Controlled Synthesis and X‐ray Analysis of Functionalized 1,2‐Diaryl‐, 1,2,3‐Triaryl‐, and 1,2,3,4‐Tetraarylbenzenes

A general, two‐step, highly efficient synthesis of 1,2‐diaryl‐, 1,2,3‐triaryl‐, and 1,2,3,4‐tetraarylbenzenes from simple stitching of α‐oxo‐ketene‐S,S‐acetals and active methylene compounds via a lactone intermediate is described. This procedure offers easy access to highly functionalized arylated benzenes that contain sterically demanding groups in good to excellent yields. The novelty of the procedure lies in the construction of aromatic compounds with the desired conformational flexibility along the molecular axis in a transition‐metal‐free environment through easily accessible precursors. Crystal analysis of these arylated benzene scaffolds showed that the peripheral aryl rings are arranged in a propeller‐like fashion with respect to the central benzene ring. Examination of the crystal packing in the structure of a 1,2,3,4‐tetraarylbenzene revealed an N???π interaction between molecules related by a two‐fold screw axis running in the direction of the a axis. Interestingly, the repeating array of N???π interactions around the axis of this 1,2,3,4‐tetraarylbenzene forces the molecules into a helical pattern.     

Pentacene nanorails on Au(110)

We studied the molecular orientation of pentacene monolayer phases on the Au(110) surface by means of near-edge X-ray absorption spectroscopy at the carbon K-shell and scanning tunneling microscopy. The highest coverage phase, displaying a (6 x 8) symmetry, is found to be formed by two types of differently oriented molecules mimicking regular arrays of nanorails. Flat-lying molecules, aligned side-by-side with the long molecular axis along the [001] direction, form long crosstie chains extending in the [110] direction. In between the adjacent flat chains, additional molecules, tilted by 90 degrees around their molecular axis, line up head-to-tail into rails extending along [110]. These molecules are very weakly hybridized with the substrate, as indicated by their lowest unoccupied molecular orbitals, which closely resemble those of the free molecule. The nanorail structure is found to be stable up to 420 K in vacuum and to also remain in place after exposure to air, thus being a template well suited for further self-assembly of organic heterostructures. The tilted quasi-free molecules open the possibility for an optimal lateral pi-coupling to other molecules or molecular assemblies.     

Solid-state packing of conjugated oligomers: from pi-stacks to the herringbone structure

The solid-state structures of a series of bithiazole and thiophene oligomers, as well as a series of substituted pentacenes, are rationalized in terms of "pitch and roll" inclinations from an "ideal" cofacial pi-stack. Pitch inclinations translate adjacent molecules relative to one another in the direction of the long molecular axis, whereas roll inclinations translate the molecules along the short molecular axis. Thus, moderately large pitch distortions preserve pi-pi interactions between adjacent molecules, whereas roll translations greater than 2.5 A essentially destroy pi-pi overlap between adjacent molecules. The familiar herringbone packing is characterized by large roll distortions. It is shown that thiophenes tend to exhibit large roll translations, whereas thiazoles have small roll but large pitch translations. Substituted pentacenes tend to have both moderate pitch and roll distances. The relationship of molecular packing to transport properties is discussed.     

β-Sheet to Helical-Sheet Evolution Induced by Topochemical Polymerization: Cross-α-Amyloid-like Packing in a Pseudoprotein with Gly-Phe-Gly Repeats

Protein-mimics are of great interest for their structure, stability, and properties. We are interested in the synthesis of protein-mimics containing triazole linkages as peptide-bond surrogate by topochemical azide-alkyne cycloaddition (TAAC) polymerization of azide- and alkyne-modified peptides. The rationally designed dipeptide N₃-CH₂CO-Phe-NHCH₂CCH ( 1 ) crystallized in a parallel β-sheet arrangement and are head-to-tail aligned in a direction perpendicular to the β-sheet-direction. Upon heating, crystals of 1 underwent single-crystal-to-single-crystal polymerization forming a triazole-linked pseudoprotein with Gly-Phe-Gly repeats. During TAAC polymerization, the pseudoprotein evolved as helical chains. These helical chains are laterally assembled by backbone hydrogen bonding in a direction perpendicular to the helical axis to form helical sheets. This interesting helical-sheet orientation in the crystal resembles the cross-α-amyloids, where α-helices are arranged laterally as sheets.     

Influence of positional isomers on the macroscale and nanoscale architectures of aggregates of racemic hydroxyoctadecanoic acids in their molecular gel, dispersion, and solid states

Inter/intramolecular hydrogen bonding of a series of hydroxystearic acids (HSAs) are investigated. Self-assembly of molecular gels obtained from these fatty acids with isomeric hydroxyl groups is influenced by the position of the secondary hydroxyl group. 2-Hydroxystearic acid (2HSA) does not form a molecular dimer, as indicated by FT-IR, and growth along the secondary axis is inhibited because the secondary hydroxyl group is unable to form intermolecular H-bonds. As well, the XRD long spacing is shorter than the dimer length of hydroxystearic acid. 3-Hydroxystearic acid (3HSA) forms an acyclic dimer, and the hydroxyl groups are unable to hydrogen bond, preventing the crystal structure from growing along the secondary axis. Finally, isomers 6HSA, 8HSA, 10HSA, 12HSA, and 14HSA have similar XRD and FT-IR patterns, suggesting that these molecules all self-assemble in a similar fashion. The monomers form a carboxylic cyclic dimer, and the secondary hydroxyl group promotes growth along the secondary axis.     

Structure, dynamics and ordering in structure i ether clathrate hydrates from single-crystal X-ray diffraction and 2H NMR spectroscopy

The structure and dynamics of trimethylene oxide (TMO) and ethylene oxide (EO) structure I (sI) hydrates are reported from single-crystal X-ray diffraction and 2H NMR spectroscopic measurements. The guest molecule positions in the large cage were determined with considerable improvement over previous diffraction work so that a dynamic model that was consistent with these orientations could be developed to explain the 2H NMR data. Reorientations are shown to take place among both symmetry-related and symmetry-independent sites, 16 positions in all. Because of the prochiral nature of the molecules, both guests show 2H NMR line shapes with large asymmetry parameters, rather unusual for guest molecules in the sI hydrate large cage. The results also show that the dipolar axis of the TMO molecule lies close to the 4 bar axis of the cage on average, whereas for EO, this is not the case. For TMO, progressive alignment of the polar axis with decrease of temperature then allows the dipoles to interact more strongly until dipole reversal is quenched at the ordering transition. The lack of ordering of EO is consistent with the much weaker alignment of the molecular dipoles along the 4 bar axis. With the new complementary information on the structure and dynamics from crystallography and NMR, it is possible to understand why the large cage guests order in the large cage of sI hydrate for TMO hydrate but not for EO hydrate.     

Three-dimensional self-assembly of metallic rods with submicron diameters using magnetic interactions

Metallic rods with submicron diameters that contain disklike ferromagnetic sections self-assemble into highly stable, hexagonally close-packed arrays of rods. The rods were fabricated by electrodeposition in porous alumina membranes and comprised alternating sections of gold and nickel. The thicknesses of the ferromagnetic nickel sections were approximately one-half the diameter of the rods (400 nm); this geometry orients the "easy" axis of magnetization perpendicular to the long axis of the rod. After magnetization of the rods with a rare-earth magnet, followed by sonication of the suspension, the rods spontaneously assembled into three-dimensional (3D) bundles that, on average, contained 15-30 rods. A macroscopic model of the rods suggests that the most stable orientation of the magnetic dipoles for rods in a defect-free, hexagonally close-packed arrangement is in concentric rings with the dipoles oriented head-to-tail. This configuration minimizes the energy of the bundle and does not generate a net dipole for the structure. This work provides a simple demonstration that magnetic interactions between ferromagnetic objects can direct and stabilize the formation of ordered, 3D structures by self-assembly.     

Formation process of cyclodextrin necklace-analysis of hydrogen bonding on a molecular level

By means of scanning tunneling microscopy (STM), we succeeded for the first time in the quantitative analysis of the intramolecular conformation of a supramolecule, cyclodextrin (CyD) necklace, driven by hydrogen bonding. Contrary to the current model, based on macroscopic analyses, which indicates that all CyDs are arranged in head-to-head or tail-to-tail (secondary-secondary or primary-primary hydrogen bonding) conformation, about 20% head-to-tail (primary-secondary hydrogen bonding) conformation was found to exist in the molecule. In addition, comparing the STM results with the theoretical model of the necklace formation, the formation ratio of the tail-to-tail and head-to-tail conformations due to the strength difference between primary-primary and primary-secondary hydrogen bonds of CyDs was directly obtained, for the first time, to be 2:1.     

Ni(II)-mediated self-assembly of artificial beta-dipeptides forming a macrocyclic tetranuclear complex with interior spaces for in-line molecular arrangement

Metal-mediated self-assembly of bioinspired molecular building blocks shows promise as an excellent strategy to provide well-defined metal arrays and nanoscopic metallo-architectures in a programmable way. Herein, we report Ni(II)-mediated self-assembly of artificial beta-dipeptides (1) which were prepared from a newly designed beta-amino acid bearing a propanediamine ligand as the side chain. The beta-dipeptide (1) has thus two sets of ligands, that is, each building block serves as a tridentate ligand with a bidentate propanediamine unit and an amide carbonyl group. Both C- and N-terminal tridentate ligands in 1 bind to two Ni(II) ions independently, and consequently, four beta-dipeptides are circularly arranged in a head-to-tail fashion to form a macrocyclic tetranuclear Ni(II) complex, Ni414(ClO4)8(H2O)10. The cyclic structure was determined by X-ray analysis and ESI-TOF mass spectrometry. The resulting unique twisted-boat structure allows the formation of isolated spaces for in-line hydrogen-bonded arrangement of water and anion molecules within a hole and two grooves rich in hydrogen bonding groups.     

Oriented Electric Fields Accelerate Diels–Alder Reactions and Control the endo/exo Selectivity

Herein we demonstrate that an external electric field (EEF) acts as an accessory catalyst/inhibitor for Diels–Alder (DA) reactions. When the EEF is oriented along the “reaction axis” (the coordinate of approach of the reactants in the reaction path), the barrier of the DA reactions is lowered by a significant amount, equivalent to rate enhancements by 4–6 orders of magnitude. Simply flipping the EEF direction has the opposite effect, and the EEF acts as an inhibitor. Additionally, an EEF oriented perpendicular to the “reaction axis” in the direction of the individual molecule dipoles can change the endo/exo selectivity, favouring one or the other depending on the positive/negative directions of the EEF vis‐à‐vis the individual molecular dipole. At some critical value of the EEF along the “reaction axis”, there is a crossover to a stepwise mechanism that involves a zwitterionic intermediate. The valence bond diagram model is used to comprehend these trends and to derive a selection rule for EEF effects on chemical reactions: an EEF aligned in the direction of the electron flow between the reactants will lower the reaction barrier. It is shown that the exo/endo control by the EEF is not associated with changes in secondary orbital interactions.     

Design of pi-conjugated organic materials for one-dimensional energy transport in nanochannels

Various end-substituted distyrylbenzenes have been synthesized to serve as guest molecules in inclusion compounds to promote efficient energy transport along one-dimensional channels. Their optical and photophysical properties have been characterized at both experimental and theoretical levels. All molecules display a large transition dipole moment between the ground state and lowest excited state and hence a short radiative lifetime (on the order of 1-2 ns). They also exhibit a large spectral overlap between the emission and absorption spectra, which enables efficient energy transport between molecules arranged in a head-to-tail configuration in nanochannels. Hopping rates on the order of 10(12) s(-1) are calculated at a full quantum-chemical level; this is much larger than the radiative lifetimes and opens the way for energy migration over large distances. Changes in the nature of the terminal substituents are found to modulate the optical properties weakly but to impact significantly the energy transfer rates.     

The influence of polytypic structures on the M011-->M101 solid-solid phase transition of n-C36H74: an application of the oblique infrared transmission method

The molecular displacements on the M011-->M101 phase transition of n-hexatriacontane (n-C36H74) have been investigated with an IR microscope designed for the oblique infrared transmission method. It has been clarified that two polytypic structures of the M011 modification, single-layered structure (Mon) and double-layered one (Orth II), both transform to the M101 modification of single-layered structure with their respective mechanisms. On the M011(Mon)-->M101 transition, the inclination direction of molecular axis is changed by 90 degrees through an intermediate state in which the molecular chain is set perpendicular to the basal plane of the single crystal. On the other hand, a polymorphic-polytypic composite structural change on the M011(Orth II)-->M101 transition is accomplished through two kinds of molecular displacements occurring alternately along the stacking direction of molecular layers.     

Antiferroelectric alignment and mechanical director rotation in a hydrogen-bonded chiral SmC* A elastomer

A new type of chiral smectic elastomer based on poly[4-(6-acryloyloxyhexyloxy)benzoic acid] is discussed. The layer structure and the molecular tilt stabilized by hydrogen bonding between side groups are identified by X-ray measurements. Well aligned and optically clear monodomain samples with smectic layers in the film plane are obtained by uniaxial stretching and then frozen-in by additional gamma-radiation crosslinking. In this monodomain state, two opposite orientations of director tilt are distributed through the sample thickness and alternate between neighbouring layers in a zigzag fashion. This structure of the stress-aligned chiral smectic C elastomer is similar to that of antiferroelectric liquid crystals of the smectic C^* _A type. Further mechanical stretching in the layer plane induces a gradual c-director reorientation along the new stress axis, when a threshold deformation ~ 20% is exceeded. The (reversible) transition proceeds as a director azimuthal rotation around the smectic C cone, with the layers essentially undistorted and the tilt angle of the side mesogenic groups preserved.     

Crystal structure of friction-transferred poly(2,5-dioctyloxy-1,4-phenylenevinylene)

Poly(2,5-dioctyloxy-1,4-phenylenevinylene) (DOPPV) was found to form a highly oriented film by a friction-transfer technique. Structural investigation of friction-transferred DOPPV was studied by means of polarized ultraviolet-visible (UV-vis) absorption spectroscopy, polarized photoluminescence (PL) spectroscopy, and synchrotron-sourced grazing incident X-ray diffraction (GIXD) analysis. The polarized UV-vis absorption and PL spectra indicate clear axial alignment. DOPPV backbones in friction-transferred film are highly aligned along the drawing direction of the friction-transfer. Further information of the molecular arrangement in friction-transferred DOPPV film was investigated by both the out-of-plane and the in-plane GIXD analyses with synchrotron source. The DOPPV molecules in friction-transferred films were perfectly arranged three-dimensionally: the backbones aligned along the drawing direction of friction-transfer, the alkyl side chains lay in the film plane, and the planar backbones were arranged parallel to the film surface. Additionally, two neighboring DOPPV molecules along the direction of inter-backbones separation by alkyl side chains were found to be shifted with respect to one another by the mean distance of half of a monomeric repeat.     

Polyfunctional inorganic-organic hybrid materials: an unusual kind of NLO active layered mixed metal oxalates with tunable magnetic properties and very large second harmonic generation

Mixed M(II)/M(III) metal oxalates, as "stripes" connected through strong hydrogen bonding by para-dimethylaminobenzaldeide (DAMBA) and water, form an organic-inorganic 2D network that enables segregation in layers of the cationic organic NLO-phore trans-4-(4-dimethylaminostyryl)-1-methylpyridinium, [DAMS+]. The crystalline hybrid materials obtained have the general formula [DAMS]4[M2M'(C2O4)6].2DAMBA.2H2O (M = Rh, Fe, Cr; M' = Mn, Zn), and their overall three-dimensional packing is non-centrosymmetric and polar, therefore suitable for second harmonic generation (SHG). All the compounds investigated are characterized by an exceptional SHG activity, due both to the large molecular quadratic hyperpolarizability of [DAMS+] and to the efficiency of the crystalline network which organizes [DAMS+] into head-to-tail arranged J-type aggregates. The tunability of the pairs of metal ions allows exploiting also the magnetic functionality of the materials. Examples containing antiferro-, ferro-, and ferri-magnetic interactions (mediated by oxalato bridges) are obtained by coupling proper M(III) ions (Fe, Cr, Rh) with M(II) (Mn, Zn). This shed light on the role of weak next-nearest-neighbor interactions and main nearest-neighbor couplings along "stripes" of mixed M(II)/M(III) metal oxalates of the organic-inorganic 2D network, thus suggesting that these hybrid materials may display isotropic 1D magnetic properties along the mixed M(II)/M(III) metal oxalates "stripes".